3D-Blast is a novel shape-density based protein structure search and alignment tool which uses the Hex docking spherical polar Fourier (SPF) correlation technique. This allows the shapes of protein domains to be superposed and compared in a completely sequence-independent way. The current version of 3D-Blast uses a database of 12,881 CATH domain structures (CATH v3.4).

The 3D-Blast server may be used to superpose the 3D structures of a given pair of proteins or to search a given protein structure against the entire CATH database to give a ranked list of similar CATH families.

This could reveal unexpected similarities between different CATH families for example. We aim to develop 3D-Blast further in order to build a novel and efficient shape-based index for the CATH database.

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Related publications
Representing and Comparing Protein Folds and Fold Families Using 3D Shape-Density Representations. L. Mavridis, A.W. Ghoorah, V. Venkatraman, and D.W. Ritchie (2011). To appear. Download 12 examples.

3D-Blast: 3D Protein Structure Alignment, Comparison, and Classification Using Spherical Polar Fourier Correlations. L. Mavridis, D.W. Ritchie (2010). Pacific Symposium on Biocomputing 15 281-292.

Funding acknowledgements
Agence Nationale de la Recherche, France

Grant reference ANR-08-CEXC-017-01

3D-Blast version July 2011